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I am trying to find the number of silent mutations in for each position in codon.

In the homework, I am asked:

For the codons and for each position, count the number of silent mutation. There are 64 codons, for each position there are 3 mutations leading to a change at the DNA level. There are thus 192 possible mutations for each of the three positions of the codons. For each position, print the number of silent mutations.

I understand stand silent mutation is the mutation that doesn't lead to amino acid change. For example, GCC can become GCT but it is still Thr

I am not sure what does "calculating silent mutation for each position" mean? I mean it is easy to find silent mutation for each codon like the example I gave above, but couldn't really understand how to calculate the silent mutation for each position.

Should I change letters (nucleotides) one by one and see if it causing a silent mutation?

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Calculate in this context would just mean determine. You don't actually have to change every base to determine whether a change is silent. Instead, try building a hash table of amino acids to codons, which you can then quickly iterate over to find all silent changes.

BTW, try to avoid loaded terms like "mutation", even if your professor incorrectly used it. Terming things like this as "silent polymorphism" or "silent change" or something along those lines is preferable.

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  • $\begingroup$ but he wants me to find number of silent mutations for each position of codon. Lets say codon is GCT and wants me to count the number of silent mutation for the codons and for each position. $\endgroup$
    – Mert Metin
    Commented Oct 9, 2017 at 19:01
  • $\begingroup$ You can efficiently get that from the method I described. $\endgroup$
    – Devon Ryan
    Commented Oct 9, 2017 at 19:41
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    $\begingroup$ @snnlaynnkrdsm try and implement this. Once you have something written down, if you're stuck with a specific aspect of your program, you can ask again here. But first try it out! We won't just write the program for you, but we're happy to help with specific problems you face. $\endgroup$
    – terdon ♦
    Commented Oct 9, 2017 at 22:01
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    $\begingroup$ Curious why you think 'mutation' is a loaded term? To me, 'silent' is the loaded part, since synonymous changes may have fitness effects due to codon usage bias or regulatory element overlapping coding sequences $\endgroup$
    – Chris_Rands
    Commented Oct 11, 2017 at 11:43
  • $\begingroup$ Patients (and scientists in my experience) tend to over interpret what a "mutation" is. Things like synonymous polymorphisms were less likely to be conveyed to non-professionals, but yes the "silent" terminology is also misleading, though it's not going to make some random patient think they're going to be the next Magneto. $\endgroup$
    – Devon Ryan
    Commented Oct 11, 2017 at 11:48

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